52796475005cb8828c73dfbb97ba9820667c9d41,cnvlib/coverage.py,,interval_coverages_pileup,#Any#Any#Any#Any#,147

Before Change

def interval_coverages_pileup(bed_fname, bam_fname, min_mapq, procs=1):
    Calculate log2 coverages in the BAM file at each interval.
    logging.info("Processing reads in %s", os.path.basename(bam_fname))
    if procs == 1:
        for chrom, start, end, gene, count, depth in bedcov(bed_fname, bam_fname,
                                                            min_mapq):
            yield [count,
                   (chrom, start, end, gene,
                    math.log(depth, 2) if depth else NULL_LOG2_COVERAGE, depth)]
        raise StopIteration

    with futures.ProcessPoolExecutor(procs) as pool:
        for biter in pool.map(_bedcov, ((bed_chrom, bam_fname, min_mapq) for
                                       bed_chrom in to_chunks(bed_fname))):
            for chrom, start, end, gene, count, depth in biter:
                yield [count,
                       (chrom, start, end, gene,
                        math.log(depth, 2) if depth else NULL_LOG2_COVERAGE, depth)]
            rm(bed_chrom)

def _bedcov(args):
    Wrapper for parallel.
    return list(bedcov(*args))

After Change

def interval_coverages_pileup(bed_fname, bam_fname, min_mapq, procs=1):
    Calculate log2 coverages in the BAM file at each interval.
    logging.info("Processing reads in %s", os.path.basename(bam_fname))
    if procs == 1:
        for count, row in bedcov(bed_fname, bam_fname, min_mapq):
            yield [count, row]
    else:
        with futures.ProcessPoolExecutor(procs) as pool:
            args_iter = ((bed_chunk, bam_fname, min_mapq)
                         for bed_chunk in to_chunks(bed_fname))
            for bed_chunk_fname, biter in pool.map(_bedcov, args_iter):
                for count, row in biter:
                    yield [count, row]
                rm(bed_chunk_fname)


def _bedcov(args):
    Wrapper for parallel.
    bed_fname = args[0]
    return bed_fname, list(bedcov(*args))

Instances